Attention based morphological guided deep learning network for neuron segmentation in electron microscopy

The accurate and automated segmentation of neurons in electron microscopy (EM) images presents a challenging problem in neuroscience. In this paper, we propose a deep learning (DL)-based neuron segmentation approach using a relatively shallow residual deconvolutional neural network (DNN) as the core. Our proposed segmentation framework differs from most EM image segmentation networks that use original images as input, as we suggest using modified morphological features with attention characteristics as input instead. We calculate Bhattacharyya distances in morphology feature space to provide attention features, which are then concatenated with the original image and used as input to the segmentation network. By attending to membrane pixels, our network efficiently highlights the discrimination between membrane boundaries and background pixels. To remove noise pixels in the segmentation map while preserving membrane boundaries in the final result, the dilated version of the output is then processed using a guided filtering scenario. Our proposed model outperforms several competing DL methods such as DeepLabv3 as well as different versions of deconvolutional neural networks on the ISBI 2012 dataset in terms of various image segmentation metrics. The proposed attention-based morphological guided framework can help advance research in neuroscience by providing an automated and accurate segmentation of neurons in EM images.